Pakistan's decision to reopen the overland supply routes into Afghanistan may be a slight boost for Washington-Islamabad ties, but there's much more wrangling ahead as the U.S. steps up its plans to withdraw from Afghanistan by the end of 2014

It never hurts to say sorry. That’s the trite lesson behind Pakistan’s confirmation on Tuesday that it was reopening ground supply routes into Afghanistan used by the U.S. and its allies to provision NATO forces there. Following a phone call with her Pakistani counterpart, U.S. Secretary of State Hillary Clinton issued a statement that amounted to something of a public apology for the U.S. role in a shootout along the Afghan border last November that claimed the lives of 24 Pakistani soldiers. That incident prompted weeks of heated protests in Pakistan, reinforced by a blockade of trucks conveying NATO matériel into Afghanistan and marked yet another climactic chapter in the turgid chronicle of the U.S.-Pakistan relationship.

In recent days, U.S. and Pakistani officials have been engaged in talks involving Pakistan’s newly installed Prime Minister Raja Pervez Ashraf — his predecessor, Yousuf Raza Gilani, was forced out of power by the country’s Supreme Court last month. The two sides seem to have brokered a workable deal: with the Pakistani routes closed, the U.S. and its NATO allies had to pursue far costlier avenues of transport, mostly via rail through Central Asia. With the cheaper routes now reopened, the U.S., according to Reuters, will pay Pakistan some $1.8 billion in military-aid arrears earlier withheld by a Congress disgruntled with Pakistani conduct following the American capture and killing of Osama bin Laden in Abbottabad last year. The Pakistanis, meanwhile, won’t levy a $5,000-per-truck toll they had earlier threatened to exact on U.S. convoys to Afghanistan. While a welcome boost for ties between Washington and Islamabad, the deal could spark a domestic backlash within Pakistan, where anti-American sentiment is high and often channeled against an unpopular civilian government.

I once again reiterated our deepest regrets for the tragic incident in Salala last November. I offered our sincere condolences to the families of the Pakistani soldiers who lost their lives. Foreign Minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives. We are sorry for the losses suffered by the Pakistani military. We are committed to working closely with Pakistan and Afghanistan to prevent this from ever happening again.

But, despite the platitudes that follow in Clinton’s statement, appealing to shared Pakistani and American commitments, a considerable gulf remains between the two. The subtext of the Salala incident — where, according to some reports, Pakistani border forces had fired upon NATO troops in Afghanistan — lies entirely in the U.S.’s profound doubts over Pakistan’s role in the war against the Taliban. Clinton’s awkward grammar after the phone call (“The Foreign Minister and I were reminded that our troops — Pakistani and American — are in a fight against a common enemy”) belies the widespread conviction that Pakistan is playing a double game, championing its efforts on the front lines fighting al-Qaeda while, at the very least, turning a blind eye to the presence of the Afghan Taliban and the shadowy Haqqani network, a fulcrum for South Asian terrorism, on its soil.

The overland supply routes are important not only for taking provisions to NATO forces in Afghanistan but now also for expediting the international coalition’s withdrawal by the end of 2014. How that endgame unfolds will shape the future of the U.S.-Pakistan relationship. At present, signs point to rockier times ahead: Pakistan’s continued tolerance of the Haqqani network is compounded by its perennial unwillingness to crack down on the Quetta shura — a grouping of Afghan Taliban elders plotting their insurgency’s campaigns in Afghanistan from across the border in Pakistani Baluchistan. The opaque, domineering Pakistani military remains an institution unto itself, casting a large shadow over a fledgling democratic government that’s already dogged by an energetic, opportunistic opposition and an activist Supreme Court. Pakistanis bristle at the American drone campaign, which has launched hundreds of strikes over the past few years on suspected Taliban targets in Pakistan’s tribal areas.

Unsurprisingly, such a volatile political environment leads to muddled strategy. Pakistan’s seeming inability to abandon its decades-old collaboration with the Taliban has vast consequences, as outlined by Ashley Tellis at the Carnegie Endowment for International Peace:

Amid the chaos that emerged after the Soviet withdrawal from Afghanistan, Pakistan settled on supporting the Afghan Taliban as its strategic instrument for securing Kabul’s compliance with its objectives. Although the Taliban were not always dependable surrogates on these matters, they appeared better than other Afghan rivals, and hence Islamabad — despite its denials — has stuck by them to this day. Whatever the intended benefits of this strategy, it has alienated both the broader Afghan populace and the government in Kabul, which now views Pakistan as a habitually hostile neighbor. It has also undermined the U.S.-led international-stabilization effort in Afghanistan, as well as hopes for a peaceful security transition — not to mention infuriated Washington, which now views Pakistan as a perfidious partner. And it has provoked heightened regional rivalry involving Afghanistan’s neighbors, especially Iran, India, the Central Asian republics and Russia, all of whom are determined to prevent a Pakistani-supported Taliban takeover of Afghanistan.

That overarching sense of Pakistan being a “perfidious partner” has narrowed the willingness of Washington to entertain Pakistani concerns in the wider region. Not so long ago, the U.S. may have tried to delicately coax India, Pakistan’s archrival, to keep its growing economic and political footprint in Afghanistan subdued. Now American officials are encouraging the opposite. The U.S. is eager to get out of Afghanistan, but it’s not keen on letting Pakistan call the shots as it did less than 20 years ago. And it will take much more than one symbolic phone call to resolve the tensions that underlie this fundamental difference of opinion.